Lec 13 | MIT 7.014 Introductory Biology, Spring 2005

Lec 13 | MIT 7.014 Introductory Biology, Spring 2005

Julia just mentioned that a few
of you had commented, when we were
talking about the genetic code, that some of you thought the
fact that it was degenerate,
it had some redundancy in it, like multiple
codons or threonine, that that was kind of cool,
and some of you thought it was sort of a waste
and would have maybe designed the thing
differently. That’s, you know,
part of when you study biology you don’t
get to design it from first principles. You found out what happened
during evolution and what got selected for. And once it gets selected for
then that gets sort of fixed in nature. If there were four nucleotides
then you could have one, two and
three-letter words. And it’s going to be a
three-letter word to have at least 20 then you’ve got some
degeneracy or redundancy, but that’s
not necessarily a bad thing. And, in fact,
if you go into the evolution of the code more
deeply, people are beginning to suspect it
evolved from a simpler one. And there actually are some
relationships between some of the codons that go back to the
similarities, the chemical similarities
between the amino acids. And it also allows some things
for some cells, for example,
if they want proteins to be present at very low levels they
will use a codon that has just a very low
level of the corresponding tRNA. And if
they want to make a lot of the protein they’ll use a tRNA that
it makes in abundance. And so it’s sort of another way
of controlling levels of proteins. There are a lot of different
subtleties in here. And also in biology redundancy
is not necessarily a bad thing. It’s just like on a space
flight, if something goes wrong and if there’s some
kind of redundant function then you’ve
got some backups, too. OK. Well, in any case,
today is a pretty interesting first part of the
lecture. I’ve heard a few people
express the view that why can’t I just teach what’s in the
textbook and get on with it? And I think this part,
for those of you who are following,
really trying to understand what I’m trying to do
with this course, I hope this will help you to
see this. Because what
I’ve talked about, this thing that Crick called
the “central dogma” which was the direction of
information flow in biology which
was from DNA to RNA to proteins. And I’ll just remind you,
although proteins do many things they
are, for example, enzymes that are
biological catalysts. And it was pretty
well-established, even by the
time I was an undergrad that this was the way information
flow went in biology and this was how it
worked. And there were various
statements in the literature that what was
true for E. coli was true
for an elephant. And it is still true today in a
broad sense that, as I’ve tried to emphasize
throughout the course, when you get down to a cellular
molecule level there’s an awful lot
in common and things look much more alike than different
compared to what we see at a more
macroscopic scale. However, that doesn’t mean
that all the details are the same. And maybe you could begin to
get a glimmering of that when I told
you that although the genetic code is
virtually universal. That almost every organism,
with only a couple very tiny
exceptions, uses exactly the same genetic code
to have nucleotides correspond to three-letter words in the
nucleic acid alphabet correspond to
particular amino acids in a protein. But the other languages that
are written in there such as the sequence to start transcribing
a gene, making an RNA copy or stop. Those are different between
different organisms. Yeah? Glycolysis enzymes are
amazingly similar. They are very clearly,
they arose once, and they have
stayed right through evolution. You could, in principle,
sometimes in evolution you get something
that creates a function and something
that starts out, and then like what they call
convergent evolution you end up with two things that
came from a different evolutionary origin
but have learned to do, let’s say, catalyze the same
biochemical reaction or something. Glycolysis came once. But if you
were to look inside E. coli or yeast,
let’s say E. coli and look at
how those enzymes are regulated, the thing that says
this is the start of a gene, start making the RNA,
it would look totally different than if
you looked in a mouse because the language,
the promoter does not have the same sequence in an E.
coli and in a human or in a mouse. And I’ll
tell you more about that today. But there were —
I want to just now tell you sort of three things that were
sort of exceptions to this general way
of thinking. Every one of them
generated a Nobel Prize. And this is a fun lecture for
me to give because the individuals
involved in all of these things had a very, very
close association with MIT. And when I told you when Crick
called this a central dogma he meant a
hypothesis, or at least an idea for
which there was not reasonable evidence. And he learned later it was
something a true believer cannot doubt. And once this gets established
it does get in the textbook and it does get in
your thinking. And so information goes
down this way. But there were a few oddities. I mean there were some
viruses that had RNA inside them. They didn’t have DNA. So how where
these handled? Well, there turned out to be
two classes of RNA virus. One that was studied quite
heavily called, it’s a
plant virus called the tobacco mosaic virus. And it had a coat. And then it had in it a piece
of RNA. Now, you can see if that virus
were to inject RNA in the cell it could encode proteins. But that genetic material has
to be copied. And the RNA was copied —
— by an RNA dependent RNA polymerase. And so it’s sort of just like
the RNA polymerase before,
except instead of using DNA as its template
it can use RNA. So that sort of somehow would
be a little loop in here about RNA being able to
copy itself that hadn’t been anticipated. And although this is an
important virus in the plant industry, for
plants and agriculture, it’s not so important for
humans. But there’s another class of
RNA viruses that are very important. And these are called
retroviruses. And the reason these are so
important is that the HIV-1 virus that’s associated with
AIDS is such a retrovirus. It’s a virus that has a coat
and it has an RNA that’s its genetic material. And the person who worked out
how this goes was a person at MIT,
Dave Baltimore. He was a colleague of
mine here for many years. He was the person who founded
the White- head Institute and got that up
and going. And he then finally,
to move up one more administrative
challenge, went to Caltech to be president. And that’s where he is today. And
David was working on this problem trying to figure out how
these retroviruses work. And they’re important. Not only the HIV-1
virus, but there are certain viruses that are associated with
cancer. In
general, what they do is they’ve picked up what’s called
an oncogene which is sort of often a
mutated version of one of your normal genes. And if that virus gets inside
one of your cells and brings in this
mutated gene it’s sort of kind of
the same consequence as mutating one of your own genes
along that progression of cancer. So it can kind of,
say, bring in a cell that screws up the control on when
cells are supposed to replicate and stop
dividing and so on. So David started to work on
these, and what he discovered was that these
viruses encoded, they had information
encoding proteins. And one of the proteins encoded
in their RNA is an enzyme he
characterized which is given the name “reverse transcriptase”. And what this can do is take an
RNA template and make the
corresponding complimentary DNA strand in this
way. So that if we took the — We’ll
just take this RNA out of the virus. What this virus encodes then is
an enzyme that’s able to take this RNA and make the
corresponding DNA copy. So there’s the original
RNA that was in the virus. There is the RNA that it
started out. And so
what is happening, if you will in that case,
is the information is flowing in the other direction. That was a marvelous discovery. And it was discovered by
someone who wasn’t willing just to take
what was in the textbooks but was trying to
figure out what could possibly be going on here. Now, the way these
viruses work then, once they’ve done this it’s not
so bad because they’ve got their information now in
the form of DNA. So this strand of DNA can be
made into a double-stranded DNA by just
using the kinds of enzymes that we’ve already talked about. A DNA
dependent DNA polymerase will be able to copy the other thing. And
now you’ve got a DNA copy of the information that used to be
in the virus. But what happens to that is
that you have a piece of the host DNA. And this viral DNA then inserts
into it, so you end up with this
situation where you have DNA from
the host, and this is the virus DNA. So this is the DNA that encodes
the information needed for the virus. And if this was our DNA then it
would be inserted that way. And
there are just a handful of health messages I’ve tried to
drive home in this thing. I mentioned smoking the other
day. If you smoke —
If you stop smoking you basically, well,
let me try another way. The
risk of smoking is about equal to the sum of everything else
you can possibly do in your life that
will affect your chances of getting
cancer, leaving aside what you inherited from mom and dad. The one
single thing to not do if you want to avoid cancer,
or to help loved ones who smoke avoid cancer,
is just don’t smoke, or if you
do smoke, stop. You freeze the risk of whatever
increased risk you’ve got, and then just live with that,
but it doesn’t keep getting worse with time. The other one is practice safe
sex, and this is why. HIV-1 is a retrovirus. If you get infected with it,
it makes a DNA copy of the RNA,
it makes the other strand of the DNA,
and it sticks itself in. So what you’ve got is your DNA
here, your DNA there. And HIV-1 is a permanent
traveling companion for the rest of your
life. There’s no way of getting that
out of there right now. All the systems for dealing
with AIDS are just managing the infection. So when someone is HIV-1
positive, they’ve got those viral genes now
permanently integrated into their DNA. So it’s extremely important
that you be aware of that,
or if you know people who don’t appreciate this
because they haven’t got so much of a biology background
that you help them understand that. OK. So I just wanted to show you,
I found one other picture last night. And this is you see all these
old scientists, right? Of course, David didn’t look
like this when he was doing his work. In fact, I think he’s fairly
cleaned up here. I found this one
in the Cold Spring Harbor archives last night. I’ve seen pictures of him
looking considerably more shaggy and perhaps
disreputable and stuff. But anyway, when David was
making all these discoveries he was still quite
a young man. I believe he got his
Nobel Prize when he was still in his thirties. And so many of these
discoveries are made by people that are not all that much older
than you. But, again, it’s trying to
understand why we know what we know
and then trying to fit other things into it. Now, the next thing I want to
tell you about that has some of this same
character, I’ve sort of told you that you have a piece of
DNA. Let’s
say there’s a gene here and this is the coding region,
and then we make a mRNA copy,
and then we use the genetic code and we
make the protein. And so if we sequence the DNA
and find the beginning of this
protein we can read along using that genetic
code and away it should go. And that was beautifully worked
out, understood, just like I sort of
finished up telling you the other
day. So Phil Sharp who got a Nobel
Prize for this work and is a colleague in the Biology
Department. He’s in the Cancer Center just
across the street from the building
I’m in. That was the cancer center that
Salvador Luria, who Jim
Watson trained with, had founded. And Phil was studying this
process. It was before we could sequence
DNA. It was in the mid ’70s. And he was
working with the tools we had then trying to map the
relationship of an RNA to a gene that was on a
virus. It was a DNA virus,
not an RNA virus, so don’t get yourself
mixed up with that. But what he had was
basically a fragment of DNA that he knew encoded the gene. So he knew
somewhere on this piece of DNA there was a gene somewhere in
here, and he had isolated the mRNA. And one way you could map,
physically see the relationship of an RNA and a
DNA would be to take, let’s just take
away one of these strands. So we have the complimentary
strand of the DNA to the RNA. And if we mix them together and
let them slowly cool down they will form
hydrogen bonds. They’ll form a
DNA-RNA hybrid just the same way two strands of DNA come on. And so if
the gene was a little shorter than the piece of DNA then you
might have expected to see something that
looked like this. And the way you’d see this,
if you looked in an electron microscope —
— perhaps it would look sort of
like this. You cannot actually see the two
strands, but you’d see a thick part. That would be the RNA duplex. So this would be just DNA. And the thick part is RNA base
paired with a single strand of DNA. You got it? That’s what textbooks said you
should have seen. And so
this is more. This is data from Phil’s paper
describing this. And
let me focus on this one in particular. That’s what
he actually saw. You guys got any idea what’s
going on? Why don’t you take a minute,
find somebody who’s near you and see if you can come up with
any ideas. Here’s the hybrid. Forget about this little bit at
the 3 prime end. That’s not a worry. Here is the thing. And this, I think,
is a piece of single stranded DNA
sticking out the end. But it looks a bit more
complicated. Any ideas? Most people put this
data in their drawers. Phil didn’t. Phil and his colleagues didn’t. What they realized was,
I’m going to try and redraw this just very
slightly to help you see what’s going on. What they were seeing was
something that looked rather like what they
were expecting. They were seeing a region of
hybrid DNA and they were seeing a region of
single-stranded DNA like this, but what it looked
like was there were little loops of single-stranded DNA
sticking out. And what Phil had discovered
was a phenomenon we now know as RNA splicing. And here’s what goes on. In bacteria,
with very few exceptions, you can look at the DNA,
you can find the open reading frame and you
can just read off the sequence of the protein. You find the ATG,
AUG, methionine codon,
and then it keeps going no stops, and finally you come
to a stop codon and you see there is the protein. So the coding
information is essentially continuous in almost all
bacterial genes. And there’s a few,
some genes like that in eukaryotes,
but many eukaryotic genes are constructed,
it’s almost as if you took the gene you’d find in a bacterium
and then you’d cut it in a bunch of
places and stuck extra DNA in between all
of the pieces. So you’d get something like
this where there’s, in the DNA there’d be coding
information. And then non-coding information
and another block of coding information. And then a block of non-coding
and say another one of coding information. So this is a double-stranded
DNA. And what
happens then when the cell makes RNA is the whole thing
gets copied into what’s known now as a
pre-messenger RNA. And so there’s a bit of coding
stuff here, there’s a bit of coding stuff
here, and there’s some more coding stuff there. But what the cell has
is sort of like your unedited footage from your family summer
vacation when you were running the video camera. And maybe you don’t want to
show everybody ever second of video that
you took during the thing. So what you do,
you get in there and you edit it. In the old days you used to
have to take the film and splice it. And now you can all do it with
iMovie or something like that. But
what you do is take the pieces of information you want,
and this is what the cell is doing. It takes this part of the RNA. And this part of the RNA,
and joins it together, and then this part. And when it’s done it has the
mRNA that now looks like the kind of mRNA
that you would find in a bacterium where you can find the
start codon. And then you could read in
three-letter words all the way through to the end of the
protein. So, in essence,
what Phil found was that in many organisms at least
there’s another step in here where
we get RNA splicing. And only after that you get
down to proteins. What was quite remarkable about
this result and why I’m kind of hammering
on it a little bit is this is the data that’s out of Phil’s
paper. You can look it up on the
Internet. Type in Phil Sharp 1977 and
you’ll find this original paper with
that figure in it. The moment Phil
realized what it was and talked about it at a meeting,
a whole lot of people suddenly sort of
almost simultaneously discovered RNA
splicing because they opened their drawers and there were all
these uninterpretable electron
micrographs they had. And they were in very short
order able to save it in the system. The
same thing was going on, but it was just confusing,
it didn’t fit, and
to some extent most people’s minds were set by this paradigm,
this central dogma as something that
a true believer cannot doubt. And you
had to have a flexible enough mind to be able to see that. And so this is an important
piece of biology that hadn’t been
anticipated. And it can be quite remarkable. I’m just going to give
you a couple of extreme examples. Well, not even extreme
examples. But just show you how much
non-coding information there can be. Factor 8 is a protein that
plays a part in blood clotting. And the
gene is 200 kilobase pairs. And the pre-mRNA is just a
direct copy, so it’s 200 kilobases. It’s just a single strand so
it’s not a base pair. And the actually spliced mRNA
when it’s done is 10 kilobases. So that means that only 5% of
the gene is coding information and 95%
of that information gets thrown away when the RNA gets spliced. And even a more extreme example
is a protein called dystrophin. This is
what’s affected in a human genetic disease known as
Duchenne Muscular Dystrophy. In this case,
the gene is two mega- base pairs. So of course then the
pre-mRNA is also two megabases but the pre-RNA is 16 kilobases. So in
this case less than 1% of the gene has coding information
for making a protein. There are a lot of interesting
reasons as to why it would be like this. One this, things can evolve
more rapidly sometimes because you have parts of proteins that
are sort of like modules and evolution
can probably connect them. In fact, it also provides ways
of regulating because we now know there
are alternative ways of splicing RNA. So you can take one RNA and
then splice it in different ways in different cells and end
up generating different proteins
that were all encoded by one particular
gene. And so it gives cells different
kinds of regulatory strategies they can use. Now, the third sort of thing
that came out that falls in this
same kind of thing of people having their
minds open and not fixed by the current understanding or bounded
by the current understanding is
the discovery that RNA can act as an
enzyme. And I’ve already talked to you
about that and I’ve told it was ribozyme, but it was discovered
by Tom Cech. Tom is currently
president of the Howard Hughes Medical Institute,
but he did his post-doctoral work at MIT with
Mary Lou Pardue. I’d been a post-doc at Berkeley
when he was just finishing his graduate work,
and I met him out there. And then he came to MIT to
do his post-doc. And a year later I got a job so
I’d become friends there and became friends when
we started here. So I had a pretty
close link to this particular story. Here’s a picture of Tom
together with Phil. That’s actually my wife right
there who was in this picture. But Tom actually looks much
more like that. He’s very colorful,
very fun, a very interesting person. But anyway,
when Tom left MIT to take a faculty position at Bolder he
was interested in trying to understand the
biochemistry of RNA splicing. And so he went — He did what a
good scientist will do. They’ll try and find an
experimental system where the question they want to address
is simple enough you can actually get
an answer. There’s a kind of way of doing
science where you pick a system that’s too complicated
and you never actually get an answer. It sounds very important
because you’re working on something that’s
important but you cannot, you don’t have the tools you
need to get to the answer. So Tom wanted to work on the
biochemistry of RNA splicing because that had just been
discovered. And so he went to a small
little tiny organism called tetrahymena. And the reason he looked at
that was because it had a ribosomal RNA,
so it was an RNA that was made in
great abundance within the organism. And
it only had one of these non-coding regions. I’ll tell you the words
for these coding and non-coding. To me they’re non-intuitive,
but I guess you should know them. The coding region is called,
the part that codes is called an
exon and the non-coding part is called an
intron. So, anyway, Tom worked on this
organism because the pre-mRNA was basically this. Or the pre-mRNA before the
splicing looked like this. This was going to give this
like that. He could get
large quantities of this RNA, so he was all set to make
extracts of the cells of this organism and then
start cooking up this RNA substrate
with all sorts of cell extracts. And then his plan was to purify
the enzymes that did the RNA
splicing. And so I first heard about
this, Tom was working on this when he was
here. And he went off to,
I guess it was Denmark to learn how to
grow this organism. Then they were back
and he was off at Bolder. And we used to play squash all
the time. And whenever I got out to
Bolder we’d try and get in a squash game. So I was out there at a meeting
and we were sitting around in the locker
room. And I said so how’s the
splicing biochemistry project going? Tom says, well,
it’s going OK, I guess. There’s only one
little problem, he says. The controls are splicing. Now, what he
meant was if you were trying to add cell extract and get this
thing to go what you would start out
with is the RNA in a tube basically. And that would be your control. And then you’d start adding
stuff to it and start looking for splicing. And what Tom was finding was
that if you just took this RNA and let it
sit in a test tube that the splicing
happened without him putting anything in. And here he was
already to find all the enzymes, the proteins that did
it. And Tom did
an absolutely gorgeous piece of science to prove that what was
happening was the RNA was catalyzing its own splicing. And he had to work very,
very hard to prove that it wasn’t a
contaminating protein. Remember we had this sort of
discussion? We
were talking about is DNA the genetic material and how would
we know that it wasn’t just a
little tiny bit of something else in our
DNA perhaps that was doing it. Tom had to go through pretty
much a similar exercise,
but this was one of these key insights that lead to
the proof that RNA could function as a catalyst,
what we now know as a ribozyme. And I’ve shown you now we now
sort of accept that the actual
ribosome itself is a ribozyme and that the
formation of the peptide bond, the thing that’s the heart of
all proteins is made by a ribozyme,
not catalyzed by ribosomes and not by a
protein. OK. So the next topic that I want
to try on which sort of we’ve already set up from this
is that if the information is all in
DNA to begin with then if you make an RNA copy you’re only
taking a segment of that information at
a time. And that gives the cells a lot
of possibilities for regulating how
they respond to the environment or just controlling what genes
are expressed. And there are basically two
kinds of strategies that are involved in these regulatory
decisions. They can either be —
Can either be reversible changes. For example,
a bacterium and a food source. If you’re a bacterium and
you’ve got enzymes that let you eat a hundred different kinds of
food and you’re in an environment
where there’s only one of them there,
you’re really wasting energy if you make the proteins to make
the other 99. So you might guess that somehow
evolution has selected for systems
that have learned how to turn on and off the things they need
to eat certain food sources depending
on whether the food source is available. We only carry umbrellas when it
rains. If you had to carry an umbrella
and a snowsuit and a surfboard, everything all the
time, it would slow you down in evolution. So the other type,
which we’ve talked about as well when we talked
about starting as a single cell and going to the 10^14 cells
that make us up, then many of those
changes, as those cells go along and
progressively more specialized need to be irreversible. And this is particularly
important in development. We don’t want a cell in our
retina suddenly deciding it should be part of a heart
and start to make a heart in the middle
of your eye or something like that. So things in development tend
to be once you’re off you’re off or
once you’re on you’re on or something. And just to give you another
little look at that picture I’ve shown you
before of the nematode. And at the time,
the first time I showed you this,
I was just trying to emphasize that we could take the
gene encoding green fluorescent protein and put it in anything
and it would go green. In this case,
Barbara Meyer who is at Berkeley now
but used to be my office-mate at MIT for many years,
what she’s done is she’s taken that green
fluorescent protein, the gene for that,
and she’s put it under the control
of a regulatory system, a gene that is
made to be expressed in the esophagus of the worm. And so even though that gene is
present in all the cells of that organism, it’s under the
control of a system that usually permits the
genes to be made that are needed for making esophagus but
not in other parts of the body. So you probably didn’t pick
that part up now but sort of take another look at
that same thing and see something
different. So how do we learn about gene
regulation? The key work,
like so many of these things, started kind of
inauspiciously, if you will. There were two French
scientists, Jacques Monod, who is a biochemist,
Francois Jacob who was a geneticist. And
they were working on the metabolism of lactose by E.
coli. Lactose is galactose,
beta 1,4 glucose. And you don’t have to know
exactly the structure. You can just remember there
were a lot of different hydroxyls,
and that was one particular linkage. And there’s
an enzyme that cleaves this into galactose and glucose. And this can
go right into glycolysis and make energy for the organism. And the galactose undergoes a
couple of different transformations,
and it can get in there as well. But in order to get at the
energy that’s in those carbohydrates,
this linkage has to be broken. And it was broken
by an enzyme called beta-galactosidase. That’s a
protein that’s able to catalyze the cleavage of those two
sugars. That’s what Jacques Monod and
Francois Jacob were studying. They
were helped out in this exercise. I guess part of the reason they
got going on this was people had
noticed for many years that if you grew E.
coli in glucose there was no beta-gal. I’m going to abbreviate this as
beta-gal just so I won’t have to keep writing the same thing. But if they grew E.
coli in lactose beta-gal was present. And they had to be able to
assay for this enzyme. And they used —
There were standard types of biochemical assays you could
use. But some chemists that helped
design a very cleaver kind of substrate
that helped them, that could be used in these
kinds of studies, and I’ll
show you one of them. What this enzyme really looks
at is it looks at, let’s see,
galactose. What it sees is sort of the
galactose side of this linkage, and then it reaches in and
catalyzes the cleavage of what’s joined to
it. And it turns out not to be
specific for whether glucose is on the
other side. It can accept substrates that
have other things as well. So some chemists made some
variants like this. This is a compound that’s
commonly known as X-gal. If you
talk about it in the lab it’s got a longer chemical name. But what happens if
beta-galactosidase is there, it’s
able to cleave this substrate so you get galactose,
which is colorless. But if you get just X,
this is colored, but up here this original
material is also colorless. So this is very convenient
because if you use a substrate such as this
you could put the cells on a plate with
this indicator. And if they are colored,
and the color is blue,
you’d know they were making beta-galactosidase. And if
you don’t see a color, you know they’re not. There are a variety of
ways of assaying for this enzyme. With that I’m just trying to
give you a little bit of flavor of
one of the different ways that they could
assay for it. Now, one of the issues was it
looked as though E. coli didn’t have any
beta-galactosidase activity if lactose was absent when growing
in glucose. And they made it if lactose was
present. Well, that would be kind
of what you would expect evolution would have figured out
how to do, only make the enzyme for
metabolizing lactose if the lactose
is present, but they had to figure out what the molecular
basis of this was. And one of the possibilities
was that the protein was made that
it was all sort of unfolded, and when the substrate came in
then it folded all around it and then
it could cleave it. Or another possibility,
which would be the kind we’re talking about now,
is the protein is not made until the lactose is present,
and then it makes it new. So they had to figure out,
between these two, which of
these two was true. When you see the lactose
present, is it just beta-galactosidase is already
made but it’s inactive, or is it being
made de novo when you add the lactose? So what they did was they grew
cells in glucose plus radioactive
C14-leucine for a long time. So all the proteins —
— were radioactive. And once they
got, that’s going for a long time. So every protein being
made is radioactive. Then they add excess unlabeled
leucine. So this means that from now on
any new proteins that are made will not be radioactive
because you’re just going to swamp out any
radioactive stuff with this. And they added glucose,
excuse me, now they added lactose to the cells. And then they isolated the
beta-gal enzyme. It was actually pretty easy
to do. It’s a huge enzyme and it’s a
tetramer. So very large. Even in
those days it was fairly easy to isolate this enzyme. And then they
looked to see is it radioactive? If it’s radioactive it was
there all along and it’s refolded to
become the active enzyme. Or if it had been only after
lactose then it would be made de novo in
response to it. And what they found was that it
was non-radioactive. Which implied that it was made
after you added the lactose. So they knew then that they
were studying a system in which a
protein was only made after the cells had
experienced a particular growth substrate. And so a lot of work
went into figuring out how this system worked. Let’s see. We’re a
little short on time. So I’ll tell you what I’ll do. I’ll
tell you, I’ll just put out quickly the mechanics of what
they saw, and we’ll start in on the
regulation on how this works. And some of you may
be able to figure it out. What we now know is that the
gene that encodes beta-galactosidase is
in a stretch of DNA that’s pretty
interesting. It’s got three genes. It’s the gene lacZ. This is the
gene for beta-galactosidase. And another gene called lacY
and lacA. There’s a promoter. That’s a start signal for
transcription. Remember that? So there’s a sequence here that
says start transcription. Down here is a terminator. Another word written in the
nucleic acid alphabet that means stop making
mRNA. And there is one long mRNA,
as you can see, that has the
peculiarity of encoding three different genes. So if you have
more than one gene in a single message then that’s
called an operon. You’ve got one mRNA. But, in any case,
so whenever beta-galactosidase was being made then RNA has to
start being made here, goes to there. And
we won’t worry about the functions of these other two
genes. But, as you might guess from
the way evolution has selected for it, they
have related activities to what beta-galactosidase does. And for
bacteria it’s a very efficient way to control the expression of
a bunch of genes at once. Then there was another gene up
here known as lacI that had a promoter and a
terminator, and it made an mRNA as well. And that mRNA encoded a protein
that’s known as the lac repressor. And what that lac repressor
does, it’s a protein that has the
ability to recognize a very, very specific
DNA sequence and bind there. And I’m just going to kind of
blow up this part of the thing. So what we have here is the,
this is the promoter here. And it happens that the binding
sequence — — for lac repressor overlaps
with the promoter. Weird, right? Maybe not. So I’ll tell you,
well, you can think about this over the weekend,
if you haven’t run into this system before. So this gene gets made all
the time. So this protein gets made all
the time. What does that
protein do if it’s just like this? Its job in life is to look for
this sequence and bind to it. If it binds to it,
it covers up the promoter. And the beta-galactosidase gene
is not expressed because the cell
cannot make mRNA. So this may seem
a little obscure, but there’s something very
important here. Now
the conditionality on whether this gene is expressed or not is
controlled by a protein, right? It’s controlled by this lac
repressor. If it’s on there the gene won’t
be made. And if it’s
off the gene now you can make it. There’s a promoter and the RNA
polymerase will see it. And so you’ve learned something
about proteins. They can bind various things. And so what lac repressor
has, it’s got a little binding site that lactose is able to
bind to and change the confirmation of the
lac repressor. So why don’t you take
those pieces of information and see if you can figure out how
the circuitry goes. Yeah? Did I do something wrong? Sorry. Oh, sorry. Excuse me. Yes, Z-Y-A. Excuse me. OK? We’ll walk
through that on Monday, but focus on the fact that if
the repressor is there and lactose isn’t,
it binds to this sequence. The repressor is made all the
time, but this repressor is something that
can tell you whether lactose is there or not. So you can put the circuit
together, OK?

5 thoughts on “Lec 13 | MIT 7.014 Introductory Biology, Spring 2005”

  1. The lecturer gives all the credit for the discovery of reverse transcriptase to David Baltimore. He forgot to mention Howard Temin (University of Wisconsin-Madison), who discovered the enzyme simultaneosly and shared the nobel prize for such discovery. Not all great research happens only at MIT.

  2. @danobeitia maybe you should try to understand the context. when talking about a bunch of MIT researchers, why throw in an unimportant caveat? golgi shared the nobel prize with cajal, and we all know what happened there.

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